tbuckley/cabot-search huggingface dataset:
PATH-06. SURVIVAL ANALYSIS FOR ADULT MIDLINE GLIOMA: DO ADULT MIDLINE GLIOMAS WITH THE H3 K27M MUTATION REALLY HAVE POOR PROGNOSIS?
Authors: Seonah Choi, In-Ho Jung, Jaejoon Lim, Ju Hyung Moon, Eui Hyun Kim, Se Hoon Kim, Seok-Gu Kang, Jong Hee Chang
Journal: Neuro-Oncology (2022)

Abstract PURPOSE Since it is known that midline located glioma with H3K27 mutation in children has a disastrous prognosis, in 2016 WHO classification, these tumors were defined as diffuse midline glioma (DMG) and classified as grade IV. A lot of papers about pediatric DMG have been published, but there are not many papers about adult DMG. In this study, we aimed to identify factors affecting the prognosis of adult midline glioma. This is the first paper to study the prognosis of adult DMG according to histological grade and is the largest study to investigate the survival of adult DMG. METHODS We reviewed the chart of adult patients diagnosed with midline glioma with H3K27M mutation after undergoing resection or biopsy among patients who visited our institution between January 2010 and December 2020. Survival analysis was performed according to tumor location, histological grading, Karnofsky Performance Scale (KPS), and age. RESULTS Among the 125 adult midline gliomas we identified, 45 (36.0%) had the H3K27M mutation. As a result of survival analysis performed on 125 adult midline gliomas, low histological grade, KPS ≥ 80, and age ≤ 60 showed significantly better survival. After adjusting for age, the difference in survival between H3K27M mutation and wildtype group was not significant. As a result of survival analysis performed on 45 DMG, low histological grade, KPS ≥ 80, total resection, and concurrent chemoradiation therapy group showed significantly better survival. CONCLUSION In adult midline glioma, disastrous prognosis due to H3K27M mutation was not observed as in children. The prognosis of adult midline gliomas is determined by histological grade, age, KPS, and extent of tumor resection. Therefore, the current WHO classification, which classifies all H3K27M mutant midline gliomas as grade IV regardless of histological diagnoses, is not suitable for adults.
TMIC-10. IDENTIFICATION, VALIDATION AND BIOLOGICAL CHARACTERIZATION OF NOVEL GLIOBLASTOMA TUMOUR MICROENVIRONMENT SUBTYPES: IMPLICATIONS FOR PRECISION IMMUNOTHERAPY
Authors: Kieron White, Kate Connor, Maxime Meylan, Antoine Bougoüin, Manuela Salvucci, Franck Bielle, Alice O’Farrell, Kieron Sweeney, Linqian Weng, Gabriele Bergers, Patrick Dicker, David Ashley, Eric S Lipp, Justin Low, Junfei Zhao, Patrick Y Wen, Robert Prins, Maite Verreault, Ahmed Idbaih, Jochen Prehn, Frederick Varn, Roel Verhaak, Catherine Sautès-Fridman, Wolf Fridman, Annette Byrne
Journal: Neuro-Oncology (2022)

Abstract New precision medicine therapies are urgently required for glioblastoma (GBM). However, to date, efforts to subtype patients based on molecular profiles, have failed to direct treatment strategies. We hypothesized that interrogation of the GBM tumor microenvironment (TME) and identification of novel TME-specific subtypes could inform new precision treatment strategies. To this end, a refined and validated microenvironment cell population (MCP)-counter method was applied to &amp;gt; 800 GBM patient tumours and validated by multiplex-immunohistochemistry. The MCP-counter deconvolution method interrogates the TME composition from transcriptomic data. Using this refined method, we classified the GLIOTRAIN(www.gliotrain.eu) IDHwt GBM cohort (n=123) into 3 novel clusters characterised by differences in TME composition and subsequently validated findings in the TCGA (n=69), CGGA (n=72) and DUKE (unpublished)(n=162) cohorts. TMEHigh tumours (30%) displayed elevated immune populations, functional orientation markers, immune checkpoint genes, and upregulated immunoregulatory pathways. Moreover, tertiary lymphoid structures were a feature of TMEHigh/mesenchymal+ patients. TMEMed (46%) tumours displayed heterogeneous immune populations and upregulated neuronal signalling pathways. TMELow (24%) tumours represented an ‘immune-desert’ group, high EGFR mutation frequency and upregulated EGFR signalling pathways. Longitudinal analysis of the GLASS cohort revealed TME-subtype transitions upon recurrence, influenced by TME composition changes. Finally, assessment of three GBM immunotherapy clinical trial cohorts revealed that TMEHigh patients treated with neo-adjuvant anti-PD1 have a significantly improved survival (P=0.04). Moreover, TMEHigh patients treated with anti-PD1 and an oncolytic virus (PVSRIPO) in the adjuvant setting, showed a trend towards improved survival (P=0.15 and P=0.056 respectively). Overall, we have established a novel TME-based classification system for application in intracranial malignancies. This system may be used to better inform a precision targeting approach in the brain tumour setting. For example, we hypothesise that patients bearing TMELow tumours may be amenable to neoadjuvant anti-TIM3 + EGFR inhibitor, TMEMed to anti-angiogenic immunotherapy, and TMEHigh patients to neoadjuvant anti-PD1 + anti-CTLA4.
NIMG-62. RADIOMIC-BASED PROGRESSION-FREE SURVIVAL STRATIFICATION OF PEDIATRIC LOW-GRADE GLIOMA IS ASSOCIATED WITH MOLECULAR ALTERATIONS
Authors: Anahita Fathi Kazerooni, Sherjeel Arif, Debanjan Haldar, Chao Zhao, Meen Chul Kim, Rachel Madhogarhia, Ariana Familiar, Sina Bagheri, Hannah Anderson, Jeffrey B Ware, Arastoo Vossough, Philip B Storm, Adam C Resnick, Christos Davatzikos, Ali Nabavizadeh
Journal: Neuro-Oncology (2022)

Abstract Pediatric low-grade glioma (pLGG) encompasses a variety of tumor subtypes with heterogeneous treatment response and relatively long progression-free survival (PFS). Radiomics may serve as a non-invasive and in-vivo tool for early prediction of PFS as a surrogate marker for treatment response and to objectively gauge the efficacy of novel treatment strategies. Here, we present a multivariate model based on radiomic features and clinical variables for risk stratification of pLGGs in terms of PFS and seek associations of the predicted risk groups and mutations in key molecular markers using data from PedCBioportal. Pre-operative multi-parametric MRI scans (T1-pre, T1-post, T2, T2-FLAIR) of 129 patients with newly diagnosed pLGG (median age, 7.76, range, 0.35-19.58 years; median PFS, 28.5, range, 1.1-124.8 months) were collected and quantitative radiomic features (n = 881) were extracted. A multivariate Cox proportional hazard’s (Cox-PH) regression model was fitted based on clinical (age, sex, and extent of tumor resection) and radiomic variables using 4-fold cross-validation. A subset of radiomic features (n = 27) that were most predictive of PFS was selected by applying Elastic Net regularization penalty during Cox-PH model fitting. High-, medium- and low-risk groups were determined based on model predictions. Cox-PH modeling showed excellent performance for prediction of PFS as suggested by the concordance index of 0.78. Radiogenomic assessment (data available in 94/129 patients) showed more enrichment of mutations in NF1 and RB1 genes in the high-risk group, as compared to the low- and medium-risk groups. We showed the potential value of radiomics in providing upfront prediction of PFS, which may further be used as an added treatment arm for early assessment of treatment response of the pLGG patients enrolled in the clinical trials. In the next step of this work, we will expand the cohort and cross-validate these results in an external cohort.
TMIC-79. MYELOID-DIRECTED TREATMENT USING THE TLR7/8 AGONIST RESIQUIMOD IMPROVES THE SURVIVAL OF MICE WITH MEDULLOBLASTOMA AND ENHANCES EFFICACY OF RADIOTHERAPY
Authors: Coral del Mar Alicea Pauneto, Duhyeong Hwang, Christopher Park, Marina Sokolsky, Timothy Gershon
Journal: Neuro-Oncology (2022)

Abstract We show the therapeutic potential of myeloid-directed immunomodulatory treatment for medulloblastoma. Patients with medulloblastoma, the most common malignant pediatric brain tumor, need new treatments, as standard therapy produces disabling neurotoxicities and fails 20% of patients. About 30% of medulloblastomas show hyperactivation of the SHH (Sonic Hedgehog) signaling pathway, and these tumors have large myeloid populations in the tumor microenvironment (TME). We analyzed whether activating toll-like receptors on these myeloid cells would slow tumor growth. Our prior single-cell RNA sequencing studies in both patient samples and mouse models showed that 10% of the cells in SHH medulloblastoma are myeloid cells and that these cells uniquely express TLR7 and TLR8. We treated mice genetically engineered to develop SHH medulloblastomas with the TLR7/8 agonist resiquimod, administered systemically either as free drug or in polyoxazoline nanoparticles (POx-resiquimod), and compared POx-resiquimod+radiotherapy to radiotherapy alone. We found that POx-resiquimod extended the survival time of mice with medulloblastoma, while free drug failed to show benefit. PK studies showed that POx-resiquimod increased tumor drug exposure, consistent with increased efficacy. Mechanistically, POx-resiquimod increases tumor myeloid populations and decreased the fraction of myeloid cells that expressed IGF1. POx-resiquimod plus radiation therapy, moreover, was superior to either POx-resiquimod alone, or radiotherapy alone. Together our data show that the TLR7/8 agonist resiquimod, delivered in nanoparticle formulation, produces a significant anti-tumor effect in SHH medulloblastoma, and increased the efficacy of radiotherapy. As radiotherapy is the mainstay of current medulloblastoma treatment, we propose that TLR7/8-agonist therapy such as resiquimod may be added to current regimens to reduce the radiation dose needed for efficacy, and to increase the fraction of successfully treated patients.
TMIC-55. IMMUNE DIGITAL-SPATIAL PROFILING AND CHARACTERIZATION OF GLIOMA MICROENVIRONMENT AFTER ADOPTIVE CELLULAR THERAPY
Authors: Laura Falceto Font, Dan Jin, Bayli DiVita Dean, Connor Francis, Alexandra Reid, Mathew Sebastian, John Figg, Kaytora Long-James, Loic Deleyrolle, Catherine Flores
Journal: Neuro-Oncology (2022)

Abstract INTRODUCTION Our group has previously shown that Adoptive Cellular Therapy (ACT) is efficacious against CNS malignancies including medulloblastoma, brain stem glioma, and glioblastoma. In this study, we characterized the spatial distribution of immune cells within the tumor microenvironment after ACT and conducted regional genomic analysis in situ to obtain insights into the underlying cellular dynamics. This method enabled us to define specific differences in gene expression within the T cells in the treated versus untreated tumors including changes in gene expression of regulatory T cell (Treg) associated genes, such as Runx1 and TGF-β. We also found a significant increase in Batf3 expression associated with therapy. METHODS We performed in situ GeoMx Digital Spatial Profiling (DSP) and whole genome transcriptomics (RNA) of murine glioma KR-158B-luciferase tumors after adoptive cellular therapy. ACT was conducted in orthotopic KR158B tumor-bearing mice. Histological slides were sent to be stained for CD45, CD3, GFP (to mark hematopoietic stem cell-derived cells) and nuclei, and processed following GeoMx DSP workflow for RNA. Overall gene expression clustering profiles were conducted using a Principal Component Analysis (PCA), and relative gene expression differences were analyzed by unpaired t-tests. RESULTS/CONCLUSIONS We observed differential expression of a substantial number of genes in the ACT-treated group compared to control. Our findings also indicate that tumors treated with ACT cluster separately from control tumors in PCA analysis. Furthermore, we found downregulation of genes associated with the suppressive properties of regulatory T cells (Runx1 and TGF-β), and upregulation of dendritic cell characteristic genes (Batf3) and antigen presentation genes (H2-Ab1) in ACT-treated tumors vs control. These findings provide insights into the immune cell dynamics and specific genes that are differentially expressed within the tumor microenvironment. This could help improve current adoptive cellular therapies to treat brain tumors.
RTID-03. DSP-0390, AN ORAL EMOPAMIL BINDING PROTEIN (EBP) INHIBITOR, IN PATIENTS WITH RECURRENT HIGH-GRADE GLIOMA: A FIRST-IN-HUMAN, PHASE 1 STUDY
Authors: David A Reardon, Yoshitaka Narita, Yoshiki Arakawa, Samuel Goldlust, George Anstass, Dragana McMullen, Edward Dow, Masataka Seki, Yudai Furuta, Gregory Song, Howard Colman
Journal: Neuro-Oncology (2022)

Abstract The brain's cells are dependent on their own biosynthesis of cholesterol as the blood-brain barrier prevents uptake from the circulation. In normal glial cells, regulation of cholesterol synthesis depends on cell density and is turned off when density exceeds a certain level. Gliomas maintain high levels of cholesterol synthesis genes to support abnormal growth. Upregulation of cholesterol synthesis genes is associated with decreased survival in patients with glioblastoma (GBM). Therefore, gliomas are potentially sensitive to cholesterol synthesis inhibition. DSP-0390, an investigational small molecule, inhibits EBP, an enzyme in one of the last, crucial steps of cholesterol biosynthesis. By inhibiting cholesterol synthesis, cytotoxicity can be induced selectively against hyperproliferative GBM cells. DSP-0390 has shown significant antitumor activity in orthotopic xenograft models of human GBM (data on file).DSP-0390 will be evaluated in a phase 1 study in patients with recurrent, high-grade glioma (NCT05023551). Key eligibility criteria: age &amp;gt;18 years; Karnofsky Performance Status score &amp;gt;70%; adequate renal, hepatic, and hematologic function. Patients must not have multifocal disease, leptomeningeal metastasis or extracranial metastasis, abnormal electrocardiograms, or significant cardiovascular disease. In Dose Escalation, 21-30 patients with World Health Organization (WHO) grade III or IV malignant glioma who progressed after &amp;gt;1 prior therapy will be enrolled. Dose level enrollment will be guided by a Bayesian Logistic Regression Model until identification of the maximum tolerated dose or recommended dose for expansion. Dose Expansion for clinical activity will enroll approximately 20-40 patients with WHO grade IV GBM who progressed after primary therapy and have measurable disease. Patients will receive oral DSP-0390 once daily. Study endpoints include safety (treatment-emergent adverse events [AEs], serious AEs, and dose-limiting toxicities), efficacy (6-month progression-free survival [PFS], objective response, PFS, duration of response, and 12-month overall survival), pharmacokinetics (PK), and pharmacodynamic biomarkers. This study is currently recruiting in the United States and Japan.
MODL-14. MODELING THE INTRATUMORAL HETEROGENEITY OF AGGRESSIVE GLIOBLASTOMA ON ORGANOTYPIC BRAIN SLICES TO OPTIMIZE TUMOR-HOMING TUMORICIDAL INSC TREATMENT
Authors: Xiaopei Zhang, Denise Dunn, Alain Valdivia, Andrew Buckley, Scott Floyd, Shawn Hingtgen, Andrew Satterlee
Journal: Neuro-Oncology (2022)

Abstract BACKGROUND Tumor-homing tumoricidal neural stem cell (tNSC) therapy is a promising new strategy that recently entered human patient testing for glioblastoma (GBM). Developing strategies for tNSC therapy to overcome intratumoral heterogeneity, variable cancer cell invasiveness, and differential drug response of GBM will be essential for efficacious treatment response in the clinical setting. We sought to create novel hybrid tumor models and investigate the impact of GBM heterogeneity on tNSC tumor response and treatment durability. METHODS We utilized organotypic brain slice explants and human cells with varied properties to generate heterogeneous GBM models ex vivo and in vivo. We first investigated the treatment response and durability of mono- and combination therapy with primary NSCs and fibroblast-derived human induced neural stem cells (iNSCs) engineered with tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) or enzyme-prodrug therapy. Next, we utilized the ex vivo models and molecular assays to explore mechanisms driving tumor adaption and escape. RESULTS Non-invasive imaging, molecular assays, and immunohistochemistry showed the new hybrid GBM models recapitulated key aspects of the clinical disease. Testing in multiple in vivo models showed that tNSC-TRAIL therapy induced robust initial inhibitions in tumor growth and significantly increased survival. However, tumors rebounded in multiple models and patterns of tumor regrowth varied with therapeutic, dose, and route of administration. We found that adjusting iNSC delivery strategies increased spatiotemporal TRAIL coverage and significantly decreased GBM volume throughout the brain, reducing tumor burden 100-fold as quantified in live ex vivo brain slices and resulting in varied impact on treatment durability and median survival across models of both solid and invasive tumors. CONCLUSIONS These studies report new hybrid models that accurately capture key aspects of GBM heterogeneity which markedly impact treatment response while demonstrating the ability of tNSC mono- and combination therapy to overcome certain aspects of heterogeneity for robust tumor kill.
TMIC-71. SPATIAL ANALYSIS OF GENETIC HETEROGENEITY AND TUMOR MICROENVIRONMENT INTERACTIONS IN GLIOBLASTOMA
Authors: Ugoma Onubogu, Roberto Salatino, Oszkar Szentirmai, Rachael Vaubel, Michalina Janiszewska
Journal: Neuro-Oncology (2022)

Abstract Genetic variation can be considered a driver of somatic evolution in glioblastoma (GBM); however, the tumor microenvironment (TME) is a key contributor to the selection process and evolutionary potential of cancer cells. Although diverse ecosystems exist in GBM which impact tumor cell fitness and characterize an aggressive pathophysiology, little is known about how genetically distinct subpopulations of GBM cells interact with the surrounding TME. Therefore, we sought to investigate how the varying clonal genotypes of GBM cells are influenced by different types of selective pressures within the TME. Our imaging-based strategy is centered around Specific-to-Allele PCR Florescence In Situ Hybridization (STAR-FISH), an in situ PCR based probe hybridization method for detection of point mutations and copy number variations at the single-cell level. Using STAR-FISH to illuminate the spatial distribution of clones with mutations in the TERT promoter, we integrated multicolor immunofluorescent staining, DNA-FISH, reflectance imaging, and computational cellular analysis methods to achieve highly-multiplexed single cell spatial profiling of intact GBM specimens. With this strategy we are able to simultaneously evaluate tumor tissues for the presence of hypoxic, angiogenic, and inflammatory niches, extracellular matrix organization, nuclear morphology, mutational status, and several oncogenic amplifications on the same slide and location. We analyzed 20 matched primary and recurrent GBM samples, imaging several distinct regions of the same tumor. Our initial results have revealed interesting and potentially novel distributions of subclones residing within specific microenvironments. These results include TERT mutation positive clones enriched in areas possessing more structured extracellular matrix, as well as unique arrangements of infiltrating immune cells in the angiogenic tumor niche. This research underscores the importance of the TME in selecting for certain phenotypes that characterize somatic evolution, highlighting novel genetic and spatial dependencies which sustain heterogeneity in GBM.
TMIC-30. EFFICIENT, QUANTITATIVE MAPPING OF TUMOR-IMMUNE NEIGHBORHOOD COMPOSITION IN GLIOBLASTOMA USING CASSATT
Authors: Asa Brockman, Rohit Khurana, Todd Bartkowiak, Madeline Hayes, Bret Mobley, Jonathan Irish, Rebecca Ihrie
Journal: Neuro-Oncology (2022)

Abstract The microenvironment surrounding brain cancer cells, and their position relative to anatomical features such as the vasculature, is a critical contributor to tumor malignancy. Immunohistochemical staining is widely used to examine such multicellular interactions, and approaches like cyclic immunohistochemistry (cycIHC), multiplexed immunofluorescence, or mass-based imaging can include up to 100 channels of interest. However, large (often &amp;gt; 50 GB) datasets from cycIHC or comparable approaches currently require an expert data scientist to concatenate open-source tools for each step of image pre-processing, registration, and segmentation, or the use of expensive proprietary software. We generated an open-source, unified, and user-friendly workflow for processing and analyzing cycIHC data - Cyclic Analysis of Single-Cell Subsets and Tissue Territories (CASSATT). CASSATT registers scanned slide images across all rounds of staining, segments individual nuclei, and scores marker expression on each detected cell. Beyond straightforward data analysis outputs such as dimensionality reduction, clustering, cell population identification and quantification, CASSATT explores the spatial relationships between cell populations via a statistical analysis module that can be applied to other high-dimensional imaging data types. In brief, it helps users identify populations of cells that interact - or do not interact - at frequencies that are greater than those occurring by chance. It also identifies specific ‘neighborhoods’ based on the cell types that surround each cell in the sample. The presence and location of these neighborhoods can be compared across slides or within distinct regions within a tissue. Within a newly generated cycIHC dataset consisting of 6 glioblastoma tissue sections processed through 8 cycles of chromogenic IHC staining, CASSATT successfully identified populations detected in parallel flow cytometry analyses and revealed specific associations between tumor and immune populations. Additional successful benchmarking was completed on a published tissue microarray dataset consisting of 107 cores processed through 18 cycles of staining and imaging.